All software
mzRecal
mzRecal recalibrates mass spectrometry (MS1) data in mzML format, using peptide identifications in mzIdentML.
- mass spectrometry
- proteomics
- Go
- Shell
- R
- + 2
NPLinker
Microbial natural products data mining by integrating genomics and metabolomics data
- Data processing
- multi-omics integration
- Python
- TeX
- Shell
- + 2
Open Computational Multiphysics
OpenCMP is a computational multiphysics software package based on the finite element method
- Computational Fluid Dynamics (CFD)
- computational Multiphysics
- diffuse interface method
- + 3
- Python
- TeX
OpenMS
OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license and runs under Windows, macOS, and Linux.
- C++
- mass spectrometry
- metabolomics
- + 1
- C++
- MAXScript
- Cython
- + 15
OpenPNM
OpenPNM is an open source project aiming to provide porous media researchers with a ready-made framework for performing a wide range of pore network simulations.
- Pore network modeling
- C++
- MAXScript
- Cython
- + 15
openPSTD
openPSTD is a Python-based research software that allows efficient and detailed calculation of sound propagation in a 2D built environment. It is especially useful as a reference tool for other developed software on acoustic sound propagation.
- Acoustics
- GPU
- python
- C++
- C
- GLSL
- + 3
PAVICS
PAVICS is a virtual laboratory facilitating the analysis of climate data. It provides access to several data collections ranging from observations, climate projections and reanalyses. It also provides a Python programming environment to analyze this data without the need to download it.
- analysis
- climate
- Climate change
- + 5
- HTML
- Jupyter Notebook
- Python
- + 3
PhenoTips
PhenoTips is a software tool that makes it easy for clinicians and researchers to draw pedigrees and collect structured phenotype data for patients with genetic disorders.
- API
- deep phenotyping
- genogram
- + 6
- Java
- JavaScript
- HTML
- + 4
Plus Toolkit
Toolkit for data acquisition, pre-processing, calibration, and real-time streaming of imaging, position tracking, and other sensor data for medical applications.
- 3D Slicer
- electromagnetic tracking
- image capture
- + 7
- C++
- C
- CMake
- + 2
PoreSpy
PoreSpy is a collection of image analysis tools used to extract information from 3D images of porous materials (typically obtained from X-ray tomography).
- image analysis
- porous media
- tomography
- Python
- C
- Shell
- + 2
PowerSensor3
PowerSensor is a low-cost, custom-built device that measures the instantaneous power consumption of GPUs and other devices at a high time resolution.
- GPU
- High performance computing
- C
- C++
- Python
- + 3
PyChelator
PyChelator is a Python-based Colab and web application for metal chelator calculations, taking into account pH, temperature, and ionic strength. The build-in constants can be used for EGTA and ATP as chelators, together with Calcium and Magnesium as metals. User-defined constants can be used.
- application
- calcium
- chelator
- + 7
- Jupyter Notebook
- JavaScript
- HTML
- + 2
qumia-train-scripts
Scripts and files related to ML training for the QUMIA project
- Machine learning
- Neuromuscular
- ultrasound imaging
- Jupyter Notebook
- Python
- Shell
ROBIST
Robust Optimization by Iterative Scenario Sampling and Statistical Testing
- optimization
- python
- Python
Rocket
Rocket is a framework for efficient execution of all-pair applications on heterogeneous platforms.
- Big data
- GPU
- High performance computing
- + 1
- Java
- Cuda
- C++
- + 2
Rucio deployment for KM3NeT
This repository contains the Rucio deployment for KM3NeT. It can be used as an example of how to deploy Rucio.
- Big data
- High performance computing
SalientDescriptor-matlab
If you need to automate your image matching tasks for the purposes of object detection or photo-identification in an easy way, the SalientDescriptor-matlab is right for you
- Image processing
- MATLAB
- HTML
SARXarray
An Xarray extension to process coregistered Single Look Complex (SLC) image stacks acquired by Synthetic Aperture Radar (SAR).
- Dask
- InSAR
- Interferometry
- + 6
- ReScript
- Python
scriptcwl
Create CWL workflows by writing a simple Python script.
- CWL
- Workflow technologies
- Python
- Common Workflow Language
self-hosted runners
Collection of resources to set up GitHub runners on self-hosted infrastructure
- High performance computing
- Shell
- Dockerfile
SimVascular
The only fully open source software package providing a complete pipeline from medical image data segmentation to patient specific blood flow simulation and analysis.
- Cardiovascular
- Fluid mechanics
- Medical image computing
- + 1
- C++
- Makefile
- Python
- + 9
sirup
Sirup is an open-source Python package that makes it easy to connect to, and rotate across, VPN servers provided by services such as ProtonVPN and Surfshark.
- ip-rotation
- openvpn
- python
- + 1
- Python
- Shell
SlicerIGT
Software toolkit for rapid development of image-guided therapy systems - for minimally invasive medical procedures, where operators rely on computer-generated images rather than direct sight of the target organs.
- 3D Slicer
- deep learning
- Medical image computing
- + 2
- C++
- Python
- CMake
snakemake-wrf
A snakemake workflow to run WRF, including pre- and postprocessing. See our blog post for a detailed description.
- geospatial
- High performance computing
- python
- + 1
- Jupyter Notebook
- Python
- Shell
TaxoTagger
DNA barcode identification, powered by semantic searching.
- Fungi
- Machine learning
- semantic search
- + 3
- Python
- Makefile
- Mustache
Umple
Umple allows generation of code in Java, PHP and other languages from a textual representation of UML state machines, associations and other modeling constructs, thus saving coding effort
- Code Generation
- Software Modeling
- State Machines
- + 1
- Java
- JavaScript
- GAP
- + 17
ValidSense
The ValidSense toolbox aims to assess the agreement between two quantitative methods using the Limits of Agreement analysis, aka the Bland-Altman analysis. Four existing variants are available. Moreover, a Longitudinal analysis is developed to assess agreement over time.
- Agreement Analysis
- Bland-Altman
- Limits of Agreement
- + 1
- Python
WAM2layers
WAM2layers is an atmospheric moisture-tracking model that can be used to determine where precipitation originally evaporated (backtracking), or where evaporated moisture eventually ends up (forward tracking).
- atmospheric rivers
- ERA5
- hydrological cycle
- + 4
- Python
- Jupyter Notebook
- Shell
Workflomics
Web platform for workflow exploration and benchmarking in bioinformatics
- Inter-operability & linked data
- Workflow technologies
- TypeScript
- CSS
- HTML
- + 1
WRF-runner
Simple shell script to run a complete WPS/WRF experiment in one go
- climate
- Forecasting
- workflow
- + 1
- Shell
Angle-and-step random walk
An Python implementation of random walk in 2D space based on agent angle orientation and step distance. It defines an agent class `Walker` capable of random walk movement based on random angle and movement step distance in a continuous 2D space.
Random walk in data frames
Collection of methods for producing random walks in two-dimensional space outputting position coordinates in data frames, including alternatives for grid and non-grid space. In R, it uses tidyverse "tibble" to construct the data frames that store trajectories.
Resource exploitation procedure
This module takes an agent and lets it decide which resources to target and exploit. The agent moves to the patch to be harvested, takes the resources and returns home
Absorption Coefficient Estimator using Domain Adaptation
Code underlying the research project: Extracting absorption coefficients from a room impulse response using a convolutional neural network with domain adaptation
- Absorption Coefficient
- domain adaptation
- Machine learning
- + 3
- Other
- Python
- Markdown
- + 1
ACDC-OpFlow
ACDC-OpFlow, Unified, Cross-Language Framework for AC/DC Optimal Power Flow Solutions
- AC/DC power systems
- Optimal Power Flow
- power electronic converters
A demand management and frequency settings model for complying to the COVID-19 capacity limits in public transport operations
A demand management and frequency settings model for complying to the COVID-19 capacity limits in public transport operations
- COVID-19
- demand management
- frequency settings
- + 3
AeoLiS v2.1.0
AeoLiS v2.1.0
- advection
- aeolian sediment transport
- coastal dunes
- + 5
Agent-based model software written for the master thesis Scaling Up, Staying Secure
Agent-based model software written for the master thesis Scaling Up, Staying Secure
- Agent based modelling and simulation (ABMS)
- CYBER SECURITY
- Distributed energy resources (DER)
- + 2
A high spatial resolution Extended Spring Indices database over American and European regions
A high spatial resolution Extended Spring Indices database over American and European regions
- Citizen Science
- Climate change
- Cloud computing
- + 4
- Python
- Markdown
- Other
Air Traffic Control Reinforcement Learning Environment
Air Traffic Control Reinforcement Learning Environment
- Air Traffic Control (ATC)
- Air traffic management (ATM)
- Reinforcement Learning (RL)
A model for modifying the public transport service patterns to account for the imposed COVID-19 capacity
A model for modifying the public transport service patterns to account for the imposed COVID-19 capacity
- capacity
- coronavirus
- COVID-19
- + 7
ANNESI: An open-source artificial neural network for estuarine salt intrusion
ANNESI: An open-source artificial neural network for estuarine salt intrusion
- estuary
- Neural Network
- salt intrusion
Application of SDDTMPC to control a unicycle
Application of SDDTMPC to control a unicycle
- MPC
- nonlinear control
- robotics
- + 2
- Matlab
- Markdown
ApPlyWood: a calculation tool supporting the design of plywood-based seismic retrofitting interventions on existing timber floors
ApPlyWood: a calculation tool supporting the design of plywood-based seismic retrofitting interventions on existing timber floors
- Architectural conservation
- Design tools
- Earthquake engineering
- + 4
APS
APS: Asses Pedestrian model Speed framework
- Computational Complexity
- Model assessment framework
- Pedestrian models
- + 1
- Python
- Other
- Markdown
- + 1
Argon Laser-Plasma Thruster - Design and Test of a Laboratory Model - Processing and Analysis Code
Argon Laser-Plasma Thruster - Design and Test of a Laboratory Model - Processing and Analysis Code
- argon
- laser
- laser-sustained plasma
- + 4
- Other
- TeX
- Jupyter Notebook
- + 5
[Artifact] Deductive Verification of Parameterized Embedded Systems modeled in SystemC
[Artifact] Deductive Verification of Parameterized Embedded Systems modeled in SystemC
- Deductive verification
- embedded systems
- parameterized systems
- + 2
Artifact for paper (Alpinist: an Annotation-Aware GPU Program Optimizer)
Artifact for paper (Alpinist: an Annotation-Aware GPU Program Optimizer)
- Annotation-aware
- Deductive verification
- GPU
- + 2